The second season begins four months after the events of Kirby Plaza. Peter Petrelli, Matt Parkman, Nathan Petrelli, and Sylar have all survived the events of the season one finale, and are trying to return to ordinary lives despite their extraordinary abilities, with the exception of Sylar, who is on a quest to regain the use of his abilities. The main plot arc of "Generations" deals with the Company and its research on the Shanti virus. This research is explored through the Company's founders, whose identities are revealed, as well as through the effects of various strains of the virus on The Haitian, Niki Sanders, Sylar, and others. An amnesiac Peter Petrelli observes the potential devastation of the virus in a future New York City. The "heroes" ultimately come together in an attempt to stop the release of a deadly strain of the virus and avert a global pandemic.

Interwoven with the main plot are several secondary plots. These include Nathan Petrelli's recovery following the events at Kirby Plaza; the journey of new characters Maya and Alejandro from Honduras to the United States, and their interaction with a powerless Sylar; Claire and Noah Bennet and their family adapting to a new life in southern California; Claire's relationship with her boyfriend West; Monica Dawson discovering her powers in New Orleans, with the help of her cousin Micah; Matt Parkman's reunion with his estranged father, leading to discovery of new abilities; the Company's manipulation of Mohinder Suresh; Ando Masahashi trying to piece together what happened to Hiro Nakamura; and Hiro's journey to Feudal Japan, where he meets his childhood hero, Takezo Kensei.

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Heroes the ordinary group of people gradually become aware that they have special abilities. Events illustrate their reactions to these powers, and how the discovery affects their personal and professional lives.